DynDom - Protein Domain Motions

Oligopeptide Abc Transporter, Periplasmic Oligopeptide- Binding Protein

(All numbering and residues are taken from first PDB file)

Run Details Domains Sequence Morph Domain Pairs Contact Graph

DynDom run details

Property	Value
Name	Oligopeptide Abc Transporter, Periplasmic Oligopeptide- Binding Protein
Conformer 1 (PDB)	1vr5 (A)
Conformer 2 (PDB)	4pfy (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	289	0.74	24 - 273 513 - 555
2	234	0.49	274 - 512

Sequence

`________________________________________________________________________________________________________________________` `1vr5(A) : HERNKTLYWGGALWSPPSNWNPFTPWNAVAGTIGLVYEPLFLYDPLNDKFEPWLAEKGEWVSNNEYVLTLRKGLRWQDGVPLTADDVVFTFEIAKKYTGISYSPVWNWLGRIERVDERT` `:` `4pfy(A) : TFERNKTLYWGGALWSPPSNWNPFTPWNAVAGTIGLVYEPLFLYDPLNDKFEPWLAEKGEWVSNNEYVLTLRKGLRWQDGVPLTADDVVFTFEIAKKYTGISYSPVWNWLGRIERVDERT` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1vr5(A) : LKFVFSDPRYQEWKQ-lINTPIVPKHIWENKTEEEVLQAANENPVGSGPYYVESWADDRCVFKKNGNWWGIRELGYDPKPERIVELRVLSNNVAVGl--kGELDWSNFFLPGVPVLKKAY` `:` `4pfy(A) : LKFVFSDPRYQEWKQMLINTPIVPKHIWENKTEEEVLQAANENPVGSGPYYVESWADDRCVFKKNGNWWGIRELGYDPKPERIVELRVLSNNVAVGMLMKGELDWSNFFLPGVPVLKKAY` `________________________________________________________________________________________________________________________` `_________273____________________________________________________________________________________________________________` `1vr5(A) : GIVTWYENAPY-lPANTAGIYINVNKYPLSIPEFRRA-aYAINPEKIVTRAYEN-vTAANPAGILPLPGY-kYYPKEVVDKYGFKYDPE-aKKILDELGFKDVNKDGFREDPNGKPFKLT` `:` `4pfy(A) : GIVTWYENAPYMLPANTAGIYINVNKYPLSIPEFRRAMAYAINPEKIVTRAYENMVTAANPAGILPLPGYMKYYPKEVVDKYGFKYDPEMAKKILDELGFKDVNKDGFREDPNGKPFKLT` `_________273____________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1vr5(A) : IECPYGWTDW-vSIQSIAEDLVKVGINVEPKYPDYSKYADDLYGGKFDLILNNFTTGVSATIWSYFNGVFYPDAVESEYSYSGNFGKYANPEVETLLDELNRSNDDAKIKEVVAKLSEIL` `:` `4pfy(A) : IECPYGWTDWMVSIQSIAEDLVKVGINVEPKYPDYSKYADDLYGGKFDLILNNFTTGVSATIWSYFNGVFYPDAVESEYSYSGNFGKYANPEVETLLDELNRSNDDAKIKEVVAKLSEIL` `________________________________________________________________________________________________________________________` `_________512_______________________________________________` `1vr5(A) : LKDLPFIPLWYNGAWFQASEAVWTNWPTEKNPYAVPIGWNGWWQLTGIKTLFGIEAK*` `:` `4pfy(A) : LKDLPFIPLWYNGAWFQASEAVWTNWPTEKNPYAVPIGWNGWWQLTGIKTLFGIEAKHH` `_________512_______________________________________________`

Morph

This morph was created using the MorphIt_Pro protein morphing technique.
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Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	19.6
Translation (A)	-0.1
Closure (%)	95.1
Bending Residues ( green )	273 - 276 512 - 513
Bending Region Analysis

Dynamic Contact Graph

Conformer 1 Contact:
Residue 1 ———› Residue 2

Conformer 2 Contact:
Residue 2 ———› Residue 1

Movement classification: Hinge

PyMOL Script

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